Help with non-manifold geometry and stl file
There were three main issues with you non-manifold mesh:

Faces going through other faces - You need to reconnect them vertex to vertex.
Disconnected edges (with gaps) - hard to notice, check for non-manifold vertices
Holes in mesh - just fill them through Vertex &gt; New Face (F)

To check for non-manifold geometry try this:

Select &gt; All by trait &gt; Non-Manifold. This will highlight all non-manifold vertices. There should be none.
Check face orientation - this will also reveal small holes and missing faces


Faces going through other faces

Disconnected edges (with gaps)